[gmx-users] potential energy of only the protein
Mark.Abraham at anu.edu.au
Tue Oct 30 14:09:21 CET 2007
sarbani chattopadhyay wrote:
> I want to get the potential energy of only the protein ie. without
> that of the
> water.'g_energy' calculates the energy from the energy file. The groups
> written for the
> "energygroups" are 'protein sol'.
> Is there any way to get the energy only of the protein?
I concur with David's warnings and suggestions.
In particular, g_energy will let you deduce the non-bonded component of
the protein-protein interactions if you run it and see what it lets you
choose. Extracting the bonded component is more involved, requiring a
tpbconv to get out just the protein, a trjconv to get out just the
protein, and then an mdrun -rerun on those subsets. Then, these numbers
aren't going to tell you anything useful that I know of.
More information about the gromacs.org_gmx-users